Single Particle LLC

What modules are available?

The command module avail will show all available modules.

[spuser@xgpu1 ~]$ module avail
--------------------------------- /usr/share/Modules/modulefiles ----------------------------------
dot  module-git  module-info  modules  null  shared  use.own

----------------------------- /spshared/modulefiles ------------------------------
cistem/1.0.0     cryolo/1.7.7.1  deepemhancer/latest  pymol/latest         scipion3/latest
conda/4.10.3   cuda/8.0        eman2/2.91           relion/gpu/2.1.0     spbin/latest
coot/0.9.5       cuda/10.1       openmpi/4.0.5        relion/gpu/3.1.3     topaz/0.2.4
cryodrgn/0.3.3b  cuda/11.2       pyem/0.5             relion/gpu/4.0.beta

See what modules have been loaded

The command module list will show what modules have been loaded.

[spuser@xgpu1 ~]$ module list
Currently Loaded Modulefiles:
 1) openmpi/4.0.5   2) cuda/8.0   3) cuda/10.1   4) relion/3.1

Load a Module

To load a module, use the command module load appname. The default version will get loaded. If you want a particular version, use module load appname/version e.g

[spuser@xgpu1 ~]$ module list
No Modulefiles Currently Loaded.

[spuser@xgpu1 ~]$ module load pyem/0.5

[spuser@xgpu1 ~]$ module list
Currently Loaded Modulefiles:
 1) pyem/0.3

Unload a Module

To unload a module, use the command module unload Appname. e.g.

[spuser@xgpu1 ~]$ module list
Currently Loaded Modulefiles:
 1) pyem/0.3

[spuser@xgpu1 ~]$ module unload pyem/0.3

Pyem, topaz, cryolo and deepEMhancer are installed in the conda environment for better use with relion, cryosparc and other software.

This document describes how to use software such as pyem (only for servers after December 16, 2021), for example:

pyem

Load the conda environment and activate pyem:

module load conda/23.11.0
module load pyem/0.5

Exit the conda environment (it needs to be executed twice, the first time to exit the pyem virtual environment, the second time to exit the conda environment):

conda deactivate
conda deactivate

topaz

Load the conda environment and activate topaz:

module load conda/23.11.0
module load topaz/0.2.5

Exit the conda environment (it needs to be executed twice, the first time to exit the topaz virtual environment, the second time to exit the conda environment):

conda deactivate
conda deactivate

cryolo

Load the conda environment and activate cryolo:

module load conda/23.11.0
module load cryolo/1.9.6

Exit the conda environment (it needs to be executed twice, the first time to exit the cryolo virtual environment, the second time to exit the conda environment):

conda deactivate
conda deactivate

deepEMhancer 

Load the conda environment and activate deepEMhancer :

module load conda/23.11.0
module load deepemhancer/2.3.0

Exit the conda environment (it needs to be executed twice, the first time to exit the deepEMhancer virtual environment, the second time to exit the conda environment):

conda deactivate
conda deactivate

cryodrgn 

Load the conda environment and activate cryodrgn :

module load conda/4.10.3
module load cryodrgn/2.3.0

Exit the conda environment (it needs to be executed twice, the first time to exit the deepEMhancer virtual environment, the second time to exit the conda environment):

conda deactivate
conda deactivate

Tips: When using conda software such as topaz, pyem, cryolo, deepEMhancer, etc., please open a new terminal; at the same time, do not open other software in the same terminal to avoid environment conflicts.

Because if these softwares are added to the system environment variables by default, it will cause many softwares to fail to run normally.

Dynamo

source /spshared/apps/dynamo/dynamo_activate_linux_shipped_MCR.sh

Peet

source /spshared/apps/peet/1.14.0/Particle/Particle.sh

ccpem

source /spshared/apps/ccpem/1.4.1/setup_ccpem.sh

Some software will not conflict with other software, you can directly use the command to open it.

Cistem

cisTEM

Pymol

pymol